diff options
Diffstat (limited to 'src/io.cpp')
| -rw-r--r-- | src/io.cpp | 30 |
1 files changed, 7 insertions, 23 deletions
@@ -47,10 +47,9 @@ #include "io.h" #endif - using namespace std; - +bool ReadHeader_io (const string &line, HEADER &header); //Print process bar void ProgressBar (string str, double p, double total) @@ -181,7 +180,7 @@ bool ReadFile_snps_header (const string &file_snps, set<string> &setSnps) //read header HEADER header; !safeGetline(infile, line).eof(); - ReadHeader (line, header); + ReadHeader_io (line, header); if (header.rs_col==0 && (header.chr_col==0 || header.pos_col==0) ) { cout<<"missing rs id in the hearder"<<endl; @@ -2501,7 +2500,7 @@ bool bgenKin (const string &file_oxford, vector<int> &indicator_snp, const int k //read header to determine which column contains which item -bool ReadHeader (const string &line, HEADER &header) +bool ReadHeader_io (const string &line, HEADER &header) { string rs_ptr[]={"rs","RS","snp","SNP","snps","SNPS","snpid","SNPID","rsid","RSID","MarkerName"}; set<string> rs_set(rs_ptr, rs_ptr+11); @@ -2636,7 +2635,7 @@ bool ReadFile_cat (const string &file_cat, map<string, size_t> &mapRS2cat, size_ //read header HEADER header; !safeGetline(infile, line).eof(); - ReadHeader (line, header); + ReadHeader_io (line, header); //use the header to count the number of categories n_vc=header.coln; @@ -3209,7 +3208,7 @@ bool ReadFile_wsnp (const string &file_wcat, const size_t n_vc, map<string, vect //read header HEADER header; !safeGetline(infile, line).eof(); - ReadHeader (line, header); + ReadHeader_io (line, header); while (!safeGetline(infile, line).eof()) { if (isBlankLine(line)) {continue;} @@ -3282,7 +3281,7 @@ void ReadFile_beta (const string &file_beta, const map<string, size_t> &mapRS2ca //read header HEADER header; !safeGetline(infile, line).eof(); - ReadHeader (line, header); + ReadHeader_io (line, header); if (header.n_col==0 ) { if ( (header.nobs_col==0 && header.nmis_col==0) && (header.ncase_col==0 && header.ncontrol_col==0) ) { @@ -3413,7 +3412,7 @@ void ReadFile_beta (const string &file_beta, const map<string, double> &mapRS2wA //read header HEADER header; !safeGetline(infile, line).eof(); - ReadHeader (line, header); + ReadHeader_io (line, header); if (header.n_col==0 ) { if ( (header.nobs_col==0 && header.nmis_col==0) && (header.ncase_col==0 && header.ncontrol_col==0) ) { @@ -3846,21 +3845,6 @@ void ReadFile_mstudy (const string &file_mstudy, gsl_matrix *Vq_mat, gsl_vector return; } - -//copied from lmm.cpp; is used in the following function compKtoV -//map a number 1-(n_cvt+2) to an index between 0 and [(n_c+2)^2+(n_c+2)]/2-1 -size_t GetabIndex (const size_t a, const size_t b, const size_t n_cvt) { - if (a>n_cvt+2 || b>n_cvt+2 || a<=0 || b<=0) {cout<<"error in GetabIndex."<<endl; return 0;} - size_t index; - size_t l, h; - if (b>a) {l=a; h=b;} else {l=b; h=a;} - - size_t n=n_cvt+2; - index=(2*n-l+2)*(l-1)/2+h-l; - - return index; -} - //read reference file void ReadFile_mref (const string &file_mref, gsl_matrix *S_mat, gsl_matrix *Svar_mat, gsl_vector *s_vec, size_t &ni) { |